Heisig's keywords aren't translations. Remember that you aren't actually learning any Japanese when you do RTK—you're learning mnemonic devices which help you to remember how to write all of the kanji in his list. This skill is supposed to help you when do you start learning Japanese.
The book does purport to teach you the meanings of characters, too, but the single keywords are not reliable translations of anything. If it were otherwise, we could say that a 弁護士 is a Valve Safeguard Gentleman, but a 弁護士 is in fact a lawyer.
In this case, he probably chose the term "employee" for 員 based on certain compounds it appears in, including the one you mentioned as well as (for example) 社員 and 店員. If we play the game of putting keywords together, we get "company member" and "store member" for these. Are these really that much better than "company employee" and "store employee"? (Note that your word 従業員 is gibberish either way—neither "accompany business member" nor "accompany business employee" makes any sense.)
The truth is, you can't learn the meanings of all the words and morphemes written with a given kanji by memorizing a single keyword. It'll work okay in some cases, but in a lot of others it won't. Instead, you need to learn what words (like べんごし) and morphemes (like いん) mean, and you can't assume that their meanings will resemble Heisig's keywords for the kanji they're written with.
So when you encounter a keyword that doesn't seem to match up with the meaning of a word or morpheme, just shrug and move on. There'll be plenty more where that came from.